title: Wordom: a user-friendly program for the analysis of molecular structures, trajectories, and free energy surfaces.
abstract: Wordom is a versatile, user-friendly, and efficient program for manipulation and analysis of molecular structures and dynamics. The following new analysis modules have been added since the publication of the original Wordom paper in 2007: assignment of secondary structure, calculation of solvent accessible surfaces, elastic network model, motion cross correlations, protein structure network, shortest intra-molecular and inter-molecular communication paths, kinetic grouping analysis, and calculation of mincut-based free energy profiles. In addition, an interface with the Python scripting language has been built and the overall performance and user accessibility enhanced. The source code of Wordom (in the C programming language) as well as documentation for usage and further development are available as an open source package under the GNU General Purpose License from http://wordom.sf.net.
authors.affiliation: Dipartimento di Chimica, University of Modena and Reggio Emilia v. Campi 183, 41125 Modena, Italy. mseeber@unimore.it
authors.forename: Michele
authors.initials: M
authors.lastname: Seeber
authors.forename: Angelo
authors.initials: A
authors.lastname: Felline
authors.forename: Francesco
authors.initials: F
authors.lastname: Raimondi
authors.forename: Stefanie
authors.initials: S
authors.lastname: Muff
authors.forename: Ran
authors.initials: R
authors.lastname: Friedman
authors.forename: Francesco
authors.initials: F
authors.lastname: Rao
authors.forename: Amedeo
authors.initials: A
authors.lastname: Caflisch
authors.forename: Francesca
authors.initials: F
authors.lastname: Fanelli
mesh_terms: D000465:Algorithms; D000818:Animals; D007700:Kinetics; D008958:Models, Molecular; D015394:Molecular Structure; D010455:Peptides / Q000737:chemistry*; D011506:Proteins / Q000737:chemistry*; D012984:Software; D013499:Surface Properties; D013816:Thermodynamics; D014732:Vibration
chemical_list: D010455:Peptides; D011506:Proteins